Structural Biology Software Database
Structural Biology Software Database

Application Index Record

Category: Molecular Dynamics
Last Update: 04-26-2006

We are pleased to announce the release of ProtoMol v2.0: an open source, object-oriented, component-based framework for molecular dynamics (MD) simulations. It supports CHARMM 19 and 28a2 force fields and is able to read and write PDB, PSF, XYZ, DCD, and several common graphics formats. ProtoMol is designed for high flexibility, ease of extendibility and maintenance, and high performance and scalability demands. We use MPI to implement atom- and force-based decompositions in a manner nearly transparent to both end-users and developers. The use of fast electrostatic force evaluation algorithms like particle mesh Ewald (PME), an O(n log n) method, and multigrid summation (MG), an O(n) method, further improve performance. In addition, MG has superior scalability when running in a parallel environment. ProtoMol contains many novel MD and Monte Carlo (MC) based methods suitable for simulation in a variety of ensembles. For example, shadow hybrid Monte Carlo (SHMC) has been shown to scale system size and MD timestep by a factor of 10 or more over hybrid Monte Carlo (HMC). Multiscale simulations may take advantage of longer timesteps by coupling multiple time-stepping algorithms with advanced integrators. Using targeted Molly, we have achieved stable timesteps of 16fs for solvated proteins. In addition, ProtoMol has been designed to interact with VMD, a visualization engine developed at the University of Illinois, which is used for displaying large biomolecular systems and running simulations in 3-D. Highlights of ProtoMol v2.0: - Average 50% performance increase versus ProtoMol 1.8.3 - Additional integrators including Shadow Hyrid Monte Carlo (SHMC), an NPT method based upon the work of Maryna, Tobias, and Klein, and an MD implementation of the isomolar-semigrand ensemble for computing phase equilibrium of mixtures. - An updated interface for adding new forces, integrators, and output methods - Improved code organization utilizing design patterns We invite you to visit the ProtoMol home page,, where C++ source code, documentation, and prebuilt binaries may be found. Operating systems natively supported include Linux, SunOS, Irix, HP-UX and Windows. For questions or comments, please feel free to contact the ProtoMol team at


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